NCBI C++ ToolKit
Classes | Functions
variation Namespace Reference

Classes

class  CHgvsParser
 
class  CVariationUtil
 
class  SFastLocSubtract
 Note: this is strand-agnostic. More...
 

Functions

 USING_SCOPE (objects)
 
CVariantPlacementSetFirstPlacement (CVariation &v)
 
void SetComputational (CVariation &variation)
 
bool SeqsMatch (const string &query, const char *text)
 
CRef< CSeq_locFindSSRLoc (const CSeq_loc &loc, const string &seq, CScope &scope)
 
void RepackageAssertedSequence (CVariation &vr)
 
void AdjustMoltype (CVariation &vr, CScope &scope)
 
template<typename T >
T AdjustHgvsCoord (T val, TSeqPos offset, bool adjust)
 
bool IsPureFuzzPoint (const CSeq_point &p)
 
CSeq_id_Handle GetUniquePrimaryTranscriptId (CBioseq_Handle &bsh)
 
bool IsLRG (CBioseq_Handle &bsh)
 
int GetDeltaLength (const CDelta_item &delta, int loc_len)
 
CVariation_inst::EType GetDelInsSubtype (int del_len, int ins_len)
 
string Ncbieaa2HgvsAA (const string &prot_str)
 
bool IsMitochondrion (CBioseq_Handle bsh)
 
bool ContainsAnyFuzz (CConstRef< CVariantPlacement > p)
 
static CRef< CVariationExceptionCreateException (const string &message, CVariationException::ECode code=static_cast< CVariationException::ECode >(0))
 
template<typename T >
static void ChangeIdsInPlace (T &container, sequence::EGetIdType id_type, CScope &scope)
 
static bool ValidExonTerminal (const set< TSeqPos > &exon_biostarts, const set< TSeqPos > &exon_biostops, TSeqPos exon_anchor_pos, int offset_pos)
 
static int GetFuzzSign (const CInt_fuzz &fuzz, int loc_sign)
 
static bool ValidExonTerminals (const set< TSeqPos > &exon_biostarts, const set< TSeqPos > &exon_biostops, const CVariantPlacement &p)
 
static void SwapLtGtFuzz (CInt_fuzz &fuzz)
 
static void ApplyOffsetFuzz (CSeq_loc &loc, const CInt_fuzz &offset_fuzz, bool is_start)
 
static CRef< CSeq_alignCreateSplicedSeqAlignFromFeat (const CSeq_feat &rna_feat)
 
template<typename T >
static bool ContainsIupacNaAmbiguities (const T &obj)
 
static bool IsRightPartial (CBioseq_Handle bsh)
 
static string Translate (const string &nuc_str, bool is_mito)
 
CVariation_inst::EType CalcInstTypeForAA (const string &prot_ref_str, const string &prot_delta_str)
 
static CVariantProperties::TEffect CalcEffectForProt (const string &prot_ref_str, const string &prot_delta_str)
 
static CVariationUtil::TSOTerms CalcSOTermsForProt (TSignedSeqPos nuc_delta_len, const string &prot_ref_str, const string &prot_variant_str)
 
static bool Contains (const CSeq_loc &a, const CSeq_loc &b, CScope *scope)
 
static CRef< CVariationCreateUnknownProtConsequenceVariation (const CVariantPlacement &nuc_p, const CSeq_feat &cds_feat, bool is_frameshifting, CScope &scope)
 
static size_t GetCommonPrefixLen (const string &a, const string &b)
 
static size_t GetCommonSuffixLen (const string &a, const string &b)
 
static bool HasProblematicExceptions (const CSeq_feat &cds_feat)
 
static bool Equals (const CVariation::TPlacements &p1, const CVariation::TPlacements &p2)
 
static bool IsRefSeqGene (const CBioseq_Handle &bsh)
 
static set< intGetFocusLocusIDs (const CBioseq_Handle &bsh)
 
CRef< CVariationInheritParentAttributes (const CVariation &child, const CVariation &parent)
 
static CRef< CDelta_itemCreateDeltaForOffset (int offset, const CInt_fuzz *fuzz)
 
static int GetSignedOffset (const CDelta_item &delta)
 
static const CInt_fuzzGetFuzz (const CDelta_item &delta)
 

Function Documentation

◆ AdjustHgvsCoord()

template<typename T >
T variation::AdjustHgvsCoord ( T  val,
TSeqPos  offset,
bool  adjust 
)

Definition at line 501 of file hgvs_parser2.cpp.

References offset, T, and val.

Referenced by variation::CHgvsParser::x_abs_pos().

◆ AdjustMoltype()

void variation::AdjustMoltype ( CVariation vr,
CScope scope 
)

◆ ApplyOffsetFuzz()

static void variation::ApplyOffsetFuzz ( CSeq_loc loc,
const CInt_fuzz offset_fuzz,
bool  is_start 
)
static

◆ CalcEffectForProt()

static CVariantProperties::TEffect variation::CalcEffectForProt ( const string prot_ref_str,
const string prot_delta_str 
)
static

◆ CalcInstTypeForAA()

CVariation_inst::EType variation::CalcInstTypeForAA ( const string prot_ref_str,
const string prot_delta_str 
)

◆ CalcSOTermsForProt()

static CVariationUtil::TSOTerms variation::CalcSOTermsForProt ( TSignedSeqPos  nuc_delta_len,
const string prot_ref_str,
const string prot_variant_str 
)
static

◆ ChangeIdsInPlace()

template<typename T >
static void variation::ChangeIdsInPlace ( T container,
sequence::EGetIdType  id_type,
CScope scope 
)
static

◆ Contains()

static bool variation::Contains ( const CSeq_loc a,
const CSeq_loc b,
CScope scope 
)
static

◆ ContainsAnyFuzz()

bool variation::ContainsAnyFuzz ( CConstRef< CVariantPlacement p)

Definition at line 823 of file hgvs_writer2.cpp.

References Begin(), false, and true.

Referenced by variation::CHgvsParser::x_AsHgvsInstExpression().

◆ ContainsIupacNaAmbiguities()

template<typename T >
static bool variation::ContainsIupacNaAmbiguities ( const T obj)
static

◆ CreateDeltaForOffset()

static CRef<CDelta_item> variation::CreateDeltaForOffset ( int  offset,
const CInt_fuzz fuzz 
)
static

◆ CreateException()

static CRef<CVariationException> variation::CreateException ( const string message,
CVariationException::ECode  code = static_cast<CVariationException::ECode>(0) 
)
static

◆ CreateSplicedSeqAlignFromFeat()

static CRef<CSeq_align> variation::CreateSplicedSeqAlignFromFeat ( const CSeq_feat rna_feat)
static

◆ CreateUnknownProtConsequenceVariation()

static CRef<CVariation> variation::CreateUnknownProtConsequenceVariation ( const CVariantPlacement nuc_p,
const CSeq_feat cds_feat,
bool  is_frameshifting,
CScope scope 
)
static

◆ Equals()

static bool variation::Equals ( const CVariation::TPlacements p1,
const CVariation::TPlacements p2 
)
static

◆ FindSSRLoc()

CRef<CSeq_loc> variation::FindSSRLoc ( const CSeq_loc loc,
const string seq,
CScope scope 
)

◆ GetCommonPrefixLen()

static size_t variation::GetCommonPrefixLen ( const string a,
const string b 
)
static

Definition at line 2355 of file variation_util2.cpp.

References a, b, and i.

Referenced by variation::CVariationUtil::TranslateNAtoAA().

◆ GetCommonSuffixLen()

static size_t variation::GetCommonSuffixLen ( const string a,
const string b 
)
static

Definition at line 2364 of file variation_util2.cpp.

References a, b, and i.

Referenced by variation::CVariationUtil::TranslateNAtoAA().

◆ GetDelInsSubtype()

CVariation_inst::EType variation::GetDelInsSubtype ( int  del_len,
int  ins_len 
)

◆ GetDeltaLength()

int variation::GetDeltaLength ( const CDelta_item delta,
int  loc_len 
)

Definition at line 1264 of file hgvs_parser2.cpp.

References delta(), GetLength(), len, and NULL.

Referenced by variation::CHgvsParser::x_delins().

◆ GetFocusLocusIDs()

static set<int> variation::GetFocusLocusIDs ( const CBioseq_Handle bsh)
static

◆ GetFuzz()

static const CInt_fuzz* variation::GetFuzz ( const CDelta_item delta)
static

◆ GetFuzzSign()

static int variation::GetFuzzSign ( const CInt_fuzz fuzz,
int  loc_sign 
)
static

◆ GetSignedOffset()

static int variation::GetSignedOffset ( const CDelta_item delta)
static

◆ GetUniquePrimaryTranscriptId()

CSeq_id_Handle variation::GetUniquePrimaryTranscriptId ( CBioseq_Handle bsh)

◆ HasProblematicExceptions()

static bool variation::HasProblematicExceptions ( const CSeq_feat cds_feat)
static

◆ InheritParentAttributes()

CRef<CVariation> variation::InheritParentAttributes ( const CVariation child,
const CVariation parent 
)

◆ IsLRG()

bool variation::IsLRG ( CBioseq_Handle bsh)

Definition at line 830 of file hgvs_parser2.cpp.

References CBioseq_Handle::GetId(), and ITERATE.

Referenced by variation::CHgvsParser::x_header().

◆ IsMitochondrion()

bool variation::IsMitochondrion ( CBioseq_Handle  bsh)

◆ IsPureFuzzPoint()

bool variation::IsPureFuzzPoint ( const CSeq_point p)

◆ IsRefSeqGene()

static bool variation::IsRefSeqGene ( const CBioseq_Handle bsh)
static

◆ IsRightPartial()

static bool variation::IsRightPartial ( CBioseq_Handle  bsh)
static

◆ Ncbieaa2HgvsAA()

string variation::Ncbieaa2HgvsAA ( const string prot_str)

◆ RepackageAssertedSequence()

void variation::RepackageAssertedSequence ( CVariation vr)

◆ SeqsMatch()

bool variation::SeqsMatch ( const string query,
const char *  text 
)

Definition at line 168 of file hgvs_parser2.cpp.

References a, b, CTempString::find(), i, query, and text().

Referenced by FindSSRLoc().

◆ SetComputational()

void variation::SetComputational ( CVariation variation)

◆ SetFirstPlacement()

CVariantPlacement& variation::SetFirstPlacement ( CVariation v)

◆ SwapLtGtFuzz()

static void variation::SwapLtGtFuzz ( CInt_fuzz fuzz)
static

◆ Translate()

static string variation::Translate ( const string nuc_str,
bool  is_mito 
)
static

◆ USING_SCOPE()

variation::USING_SCOPE ( objects  )

◆ ValidExonTerminal()

static bool variation::ValidExonTerminal ( const set< TSeqPos > &  exon_biostarts,
const set< TSeqPos > &  exon_biostops,
TSeqPos  exon_anchor_pos,
int  offset_pos 
)
static

Definition at line 152 of file variation_util2.cpp.

References set< Key, Compare >::end(), and set< Key, Compare >::find().

Referenced by ValidExonTerminals().

◆ ValidExonTerminals()

static bool variation::ValidExonTerminals ( const set< TSeqPos > &  exon_biostarts,
const set< TSeqPos > &  exon_biostops,
const CVariantPlacement p 
)
static
Modified on Tue Apr 16 20:13:18 2024 by modify_doxy.py rev. 669887